% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 02/04/04_14:53:24 % (c) 1992-2001 Regents of the University of California, Santa Cruz % % Sequence Alignment and Modeling Software System % http://www.cse.ucsc.edu/research/compbio/sam.html % % ----------------- Citations (SAM, SAM-T2K, HMMs) -------------------- % R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: % Extension and analysis of the basic method, CABIOS 12:95-107, 1996. % K. Karplus, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR217W.t2k-100-30-CB_burial_14_7 Host: cc85 Thu Feb 26 22:16:18 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR217W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR217W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR217W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 9381 sequences, 2218509 residues, 2040 nodes, 2961.31 seconds % % Sequence scores selected if better than: % E-value (Emax 4.0e+01) (select_score=4) % % Simple: NLL-NULL using FIM probabilities % Reverse: NLL-NULL for the reverse sequence NULL model % Calculated when Simple < simple_threshold (0.00) % E-value on N (=8162) sequences: % N / (1 + exp(-(lambda(=1.6005) * Reverse)^tau(=0.8014))) % Calculated when Simple < simple_threshold (0.00) % Rescale E-values or use -dbsize for multiple scoring runs. % Scores sorted by E-value, best first % % Sequence ID Length Simple Reverse E-value X count 1t1dA 100 -42.46 -25.75 2.28e-05 1a68 95 -40.44 -23.02 1.24e-04 1dsxA 87 -39.72 -22.78 1.44e-04 1ncx 162 -48.16 -17.14 5.50e-03 1top 162 -47.39 -15.92 1.24e-02 1nn7A 105 -35.41 -15.33 1.85e-02 1k94A 165 -29.47 -14.00 4.60e-02 1bl8A 97 -24.66 -13.27 7.67e-02 1zac 90 -30.44 -12.98 9.36e-02 1jvmA 125 -24.11 -11.65 2.42e-01 1f4qA 165 -27.55 -11.55 2.59e-01 1j95A 125 -24.26 -11.53 2.62e-01 1k4cC 124 -24.54 -11.46 2.77e-01 1r3jC 124 -24.61 -11.37 2.95e-01 3kvt 115 -28.25 -11.15 3.45e-01 1cojA 212 -32.08 -9.87 8.84e-01 1oyeA 1049 -39.24 -9.81 9.20e-01 1j7rA 86 -29.76 -9.54 1.12e+00 1hqsA 423 -32.10 -9.32 1.33e+00 1iwgA 1053 -38.38 -9.25 1.40e+00 1ggwA 140 -33.96 -9.25 1.41e+00 1byyA 53 -25.86 -9.09 1.58e+00 1mgn 154 -25.09 -8.75 2.04e+00 1okrA 123 -33.95 -8.47 2.52e+00 1h0cA 392 -25.21 -8.32 2.84e+00 1jeqB 565 -53.11 -8.25 3.01e+00 9wgaA 171 -31.36 -8.02 3.58e+00 1eswA 500 -24.47 -7.99 3.66e+00 1cwyA 500 -24.49 -7.89 3.97e+00 1auiA 521 -33.33 -7.88 3.97e+00 1mbd 153 -24.63 -7.84 4.11e+00 1bzpA 153 -24.98 -7.74 4.45e+00 1j7nB 776 -48.74 -7.59 4.98e+00 1wgtA 186 -32.68 -7.45 5.57e+00 1alvA 173 -29.14 -7.37 5.95e+00 2mysB 166 -37.76 -7.36 5.98e+00 1a6m 151 -23.27 -7.36 6.00e+00 1ik9A 213 -47.28 -7.28 6.35e+00 2spo 154 -23.63 -7.25 6.53e+00 1hqvA 191 -27.75 -7.05 7.64e+00 1j7nA 776 -48.10 -6.88 8.73e+00 1fo4A 1332 -52.75 -6.77 9.55e+00 1br1B 150 -33.44 -6.71 1.00e+01 1ddzA 496 -32.03 -6.69 1.02e+01 1e3oC 160 -28.02 -6.68 1.02e+01 1myf 153 -22.19 -6.66 1.04e+01 1irl 133 -23.73 -6.61 1.09e+01 1hev 43 -20.90 -6.38 1.31e+01 1kpkA 473 -21.10 -6.37 1.31e+01 1cqwA 295 -19.79 -6.36 1.33e+01 1q9bA 43 -21.32 -6.34 1.35e+01 1tag 324 -23.13 -6.25 1.45e+01 1dceA 567 -30.46 -6.17 1.54e+01 1bn6A 294 -19.96 -6.09 1.66e+01 1p0hA 318 -20.87 -6.07 1.67e+01 2aaa 484 -26.88 -6.03 1.74e+01 1fvzA 271 -28.57 -6.00 1.78e+01 1lrzA 426 -35.75 -5.95 1.85e+01 1f61A 429 -29.66 -5.93 1.89e+01 1jeyB 565 -52.52 -5.91 1.91e+01 1qtrA 317 -19.43 -5.90 1.92e+01 1cii 602 -49.49 -5.89 1.95e+01 1f6fA 199 -23.58 -5.87 1.98e+01 1f8rA 498 -27.84 -5.85 2.01e+01 1e6fA 143 -19.33 -5.84 2.03e+01 1fcyA 236 -21.23 -5.78 2.12e+01 1o1fC 147 -33.23 -5.69 2.30e+01 1kfuS 184 -26.33 -5.68 2.31e+01 1oglA 283 -22.46 -5.65 2.37e+01 1gp0A 143 -19.60 -5.64 2.38e+01 1ddf 127 -25.80 -5.64 2.39e+01 1mml 265 -24.33 -5.62 2.43e+01 1m2kA 249 -20.87 -5.59 2.49e+01 1i4nA 251 -22.41 -5.58 2.50e+01 1bn7A 294 -19.92 -5.57 2.52e+01 1o0wA 252 -23.66 -5.56 2.55e+01 1nx8A 273 -19.09 -5.47 2.74e+01 1agnA 373 -26.52 -5.46 2.77e+01 1q1hA 110 -21.54 -5.39 2.92e+01 1avsA 90 -28.09 -5.36 3.00e+01 4lbd 267 -21.86 -5.36 3.01e+01 1dxrL 273 -24.75 -5.33 3.10e+01 1qj5A 429 -21.23 -5.30 3.17e+01 1fu1B 203 -40.69 -5.28 3.21e+01 1lj2A 110 -37.26 -5.23 3.36e+01 3erk 364 -24.48 -5.19 3.48e+01 6prcL 273 -24.71 -5.17 3.52e+01 1tadA 324 -21.90 -5.10 3.75e+01 1k7hA 476 -31.71 -5.10 3.75e+01 1cll 148 -40.77 -5.09 3.78e+01 1ulmA 82 -25.27 -5.09 3.78e+01 1ggzA 148 -40.07 -5.07 3.85e+01 1cv2A 296 -18.12 -5.03 3.96e+01 1iz7A 295 -18.04 -5.03 3.97e+01